snapCGH package - processCGH
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@henrique-proenca-2762
Last seen 8.0 years ago
Hello, I am doing some analysis of Agilent CGH and I found out that if I have some data without duplicates the function processCGH crashes. > Error in processCGH(MA, method.of.averaging = methodOfAveraging, ID = meanIDcol, : > object "segList" not found > In addition: Warning message: > In getChrInfo(MA) : NAs introduced by coercion Analyzing the function processCGH, I found out that the error could be related with a miss location of a "}" I mean, instead of being after the following code dupl <- duplicated(MA$genes$ID) segList <- list() segList$M.observed <- MA$M[!dupl, , drop = FALSE] segList$genes <- MA$genes[!dupl, ] } The if (any(tbl > 1)) should be closed before: } dupl <- duplicated(MA$genes$ID) segList <- list() segList$M.observed <- MA$M[!dupl, , drop = FALSE] segList$genes <- MA$genes[!dupl, ] If I change the code, it seems to work, could you please tell me if this is a bug? My System information is: R version 2.7.0 (2008-04-22) i386-pc-mingw32 attached base packages: [1] splines grid tools stats graphics grDevices utils datasets methods base other attached packages: [1] snapCGH_1.8.0 RUnit_0.4.17 aCGH_1.14.0 sma_0.5.15 multtest_1.20.0 [6] cluster_1.11.10 GLAD_1.16.0 DNAcopy_1.14.0 tilingArray_1.18.0 pixmap_0.4-7 [11] geneplotter_1.18.0 annotate_1.18.0 xtable_1.5-2 AnnotationDbi_1.2.0 RSQLite_0.6-8 [16] DBI_0.2-4 genefilter_1.20.0 survival_2.34-1 vsn_3.6.0 limma_2.14.0 [21] lattice_0.17-6 strucchange_1.3-3 sandwich_2.1-0 zoo_1.5-3 RColorBrewer_1.0-2 [26] affy_1.18.0 preprocessCore_1.2.0 affyio_1.8.0 Biobase_2.0.0 loaded via a namespace (and not attached): [1] KernSmooth_2.22-22 Thanks in advance. Sorry to send you this email, but I didn't find the email of the snapCGH package maintainer. -- Regards Henrique Proen?a
CGH CGH • 518 views
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